TaxonTabReader.java

package org.phenoscape.io;

import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.io.LineNumberReader;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

import org.obo.annotation.base.TermSet;
import org.obo.app.util.Collections;
import org.obo.datamodel.OBOClass;
import org.obo.datamodel.OBOObject;
import org.obo.datamodel.OBOSession;
import org.phenoscape.model.DataSet;
import org.phenoscape.model.Specimen;
import org.phenoscape.model.Taxon;

public class TaxonTabReader {

    private final OBOSession session;
    private final TermSet collections;
    private final List<Taxon> taxa = new ArrayList<Taxon>();

    public TaxonTabReader(File aFile, OBOSession session, TermSet collections) throws IOException {
        this.session = session;
        this.collections = collections;
        this.parse(aFile);
    }

    public List<Taxon> getTaxa() {
        return this.taxa;
    }

    public DataSet getDataSet() {
        final DataSet data = new DataSet();
        data.getTaxa().addAll(this.taxa);
        return data;
    }

    private void parse(File aFile) throws IOException {
        final LineNumberReader reader = new LineNumberReader(new FileReader(aFile));
        final String header = reader.readLine();
        final List<String> fields = Arrays.asList(header.split("\t"));
        while (true) {
            final String line = reader.readLine();
            if (line == null) break;
            if (line.trim().equals("")) continue;
            final Taxon taxon = new Taxon();
            final String[] cells = line.split("\t", -1);
            final String taxonID = Collections.get(cells, fields.indexOf("Valid Taxon ID"));
            taxon.setValidName((OBOClass)(session.getObject(taxonID)));
            final String pubName = Collections.get(cells, fields.indexOf("Publication Taxon"));
            taxon.setPublicationName("".equals(pubName) ? null : pubName);
            final String comments = Collections.get(cells, fields.indexOf("Taxon Comments"));
            taxon.setComment(comments);
            final String specimensString = Collections.get(cells, fields.indexOf("Specimens"));
            if ((specimensString != null) && (!specimensString.equals(""))) {
                final String[] specimens = specimensString.split(",");
                for (String specimenString : specimens) {
                    final Specimen specimen = new Specimen();
                    String adjustedString = specimenString;
                    if (specimenString.equals("\"\"")) { continue; }
                    if (specimenString.startsWith("\"")) { adjustedString = adjustedString.split("\"")[1]; }
                    final String[] pieces = adjustedString.split(" ");
                    if (pieces.length > 0) {
                        final String collectionName = pieces[0];
                        String collectionID = null;
                        for (OBOObject term : collections.getTerms()) {
                            if (term.getName().equals(collectionName)) {
                                collectionID = term.getID();
                                break;
                            }
                        }
                        specimen.setCollectionCode((OBOClass)(session.getObject(collectionID)));
                    }
                    if (pieces.length > 1) {
                        final String catalogNum = pieces[1];
                        specimen.setCatalogID(catalogNum.trim());
                    }
                    taxon.addSpecimen(specimen);
                }
            }

            this.taxa.add(taxon);
        }
    }

}